diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst index 45f4782222..87d3212259 100644 --- a/doc/htmldoc/connect_nest/nest_server.rst +++ b/doc/htmldoc/connect_nest/nest_server.rst @@ -79,9 +79,9 @@ consideration, each of the restrictions can be disabled by setting a correspondi * ``NEST_SERVER_DISABLE_AUTH``: By default, the NEST Server requires a NESTServerAuth tokens. Setting this variable to ``1`` disables this restriction. A token is automatically created and printed to the console by NEST Server upon start-up. If needed, a custom token can be set using the environment variable ``NEST_SERVER_ACCESS_TOKEN`` -* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see `CORS - `_). Other hosts can be explicitly allowed by supplying them - in the form `http://host_or_ip:*`` to this variable (By default: http://localhost:*). +* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see + `CORS `_). Other hosts can be explicitly allowed by supplying them + in the form http://host_or_ip:\* to this variable (By default: http://localhost:\*). * ``NEST_SERVER_ENABLE_EXEC_CALL``: By default, NEST Server only allows calls to its PyNEST-like API. If the use-case requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION. diff --git a/doc/htmldoc/devices/index.rst b/doc/htmldoc/devices/index.rst index 1176894c5c..4477c36a7c 100644 --- a/doc/htmldoc/devices/index.rst +++ b/doc/htmldoc/devices/index.rst @@ -8,7 +8,7 @@ All about devices in NEST .. grid-item-card:: Stimulate the network :class-title: sd-d-flex-row sd-align-minor-center - :link: stimuate_network + :link: stimulate_network :link-type: ref .. grid-item-card:: Get data from simulation diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst index 2bf2698ac4..277ac2e933 100644 --- a/doc/htmldoc/get-started_index.rst +++ b/doc/htmldoc/get-started_index.rst @@ -232,8 +232,6 @@ More topics .. toctree:: :hidden: - understand_index - .. |nav| image:: static/img/GPS-Settings-256_nest.svg .. |script| image:: static/img/script_white.svg :scale: 20% diff --git a/doc/htmldoc/related_projects.rst b/doc/htmldoc/related_projects.rst index 1bcd309ab5..06b5005e92 100644 --- a/doc/htmldoc/related_projects.rst +++ b/doc/htmldoc/related_projects.rst @@ -90,10 +90,10 @@ real-time operation. TheVirtualBrain (TVB) --------------------- -:ref:`TVB ` is a framework for the simulation of the dynamics of large-scale brain networks with +:ref:`TVB ` is a framework for the simulation of the dynamics of large-scale brain networks with biologically realistic connectivity. -* :ref:`Get started with TVB ` +* :ref:`Get started with TVB ` ConnPlotter ----------- diff --git a/doc/htmldoc/synapses/synapse_specification.rst b/doc/htmldoc/synapses/synapse_specification.rst index f12abd2b95..c42038fbf1 100644 --- a/doc/htmldoc/synapses/synapse_specification.rst +++ b/doc/htmldoc/synapses/synapse_specification.rst @@ -65,7 +65,7 @@ Array parameters Array parameters can be used with the rules ``one_to_one``, ``all_to_all``, ``fixed_total_number``, ``fixed_indegree``, and ``fixed_outdegree``. -For details on connection rules, see :ref:`connectivity_concept`. +For details on connection rules, see :ref:`connectivity_concepts`. The arrays can be specified as NumPy arrays or Python lists. As with the scalar parameters, all parameters have to be specified as arrays of the correct type. diff --git a/models/iaf_psc_delta.h b/models/iaf_psc_delta.h index 2bc4fadf8a..b27e1ee035 100644 --- a/models/iaf_psc_delta.h +++ b/models/iaf_psc_delta.h @@ -121,6 +121,10 @@ hyperpolarization to biophysically plausible values, set parameter .. note:: + + NEST uses exact integration [1]_, [2]_ to integrate subthreshold membrane + dynamics. + Spikes arriving while the neuron is refractory, are discarded by default. If the property ``refractory_input`` is set to True, such spikes are added to the membrane potential at the end of the diff --git a/nestkernel/recording_backend_ascii.h b/nestkernel/recording_backend_ascii.h index 7ec7d74b62..9b0c93915f 100644 --- a/nestkernel/recording_backend_ascii.h +++ b/nestkernel/recording_backend_ascii.h @@ -46,7 +46,7 @@ each MPI process. This can cause a high load on the file system in large simulations. This backend can become prohibitively inefficient, particularly on machines with distributed filesystems. In case you experience such scaling problems, the :doc:`recording backend for -SIONlib ` may be a possible alternative. +SIONlib ` may be a possible alternative. Filenames of data files are determined according to the following pattern: diff --git a/nestkernel/recording_backend_sionlib.h b/nestkernel/recording_backend_sionlib.h index 40e6ddf183..ea7ea77753 100644 --- a/nestkernel/recording_backend_sionlib.h +++ b/nestkernel/recording_backend_sionlib.h @@ -47,7 +47,7 @@ a binary container file (or to a rather small set of such files). This is especially useful for large-scale simulations running in a distributed way on many MPI processes/OpenMP threads. In such usage scenarios, writing to plain text files (see :doc:`recording backend -for ASCII files `) would cause a large +for ASCII files `) would cause a large overhead because of the huge number of generated files and thus be very inefficient. diff --git a/pynest/examples/EI_clustered_network/README.rst b/pynest/examples/EI_clustered_network/README.rst index 4f7d5a43d7..75d3961457 100644 --- a/pynest/examples/EI_clustered_network/README.rst +++ b/pynest/examples/EI_clustered_network/README.rst @@ -16,24 +16,24 @@ If you use this code, we ask you to cite the paper by Rostami et al. [1]_ and th File structure -------------- -* :doc:`run_simulation.py `: an example script to try out the EI-clustered circuit model -* :doc:`network.py `: the main ``Network`` class with functions to build and simulate the network -* :doc:`helper.py `: helper functions for calculation of synaptic weights and currents and plot function for raster plots -* :doc:`network_params.py `: network and neuron parameters -* :doc:`stimulus_params.py `: parameters for optional external stimulation -* :doc:`sim_params.py `: simulation parameters +* :doc:`run_simulation_EI.py `: an example script to try out the EI-clustered circuit model +* :doc:`network_EI.py `: the main ``Network`` class with functions to build and simulate the network +* :doc:`helper_EI.py `: helper functions for calculation of synaptic weights and currents and plot function for raster plots +* :doc:`network_params_EI.py `: network and neuron parameters +* :doc:`stimulus_params_EI.py `: parameters for optional external stimulation +* :doc:`sim_params_EI.py `: simulation parameters Running the simulation ---------------------- .. code-block:: bash - python run_simulation.py + python run_simulation_EI.py A raster plot of the network activity is saved as ``clustered_ei_raster.png``. The code can be parallelized by using multiple threads during the NEST simulation. -This can be done by setting the parameter ``n_vp`` in the ``run_simulation.py`` script. +This can be done by setting the parameter ``n_vp`` in the ``run_simulation_EI.py`` script. Contributions to this PyNEST model implementation ------------------------------------------------- diff --git a/pynest/examples/EI_clustered_network/helper.py b/pynest/examples/EI_clustered_network/helper_EI.py similarity index 99% rename from pynest/examples/EI_clustered_network/helper.py rename to pynest/examples/EI_clustered_network/helper_EI.py index 902535849e..7ae6447d9c 100644 --- a/pynest/examples/EI_clustered_network/helper.py +++ b/pynest/examples/EI_clustered_network/helper_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# helper.py +# helper_EI.py # # This file is part of NEST. # diff --git a/pynest/examples/EI_clustered_network/network.py b/pynest/examples/EI_clustered_network/network_EI.py similarity index 99% rename from pynest/examples/EI_clustered_network/network.py rename to pynest/examples/EI_clustered_network/network_EI.py index 306014db17..aa7a4fe7c1 100644 --- a/pynest/examples/EI_clustered_network/network.py +++ b/pynest/examples/EI_clustered_network/network_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# network.py +# network_EI.py # # This file is part of NEST. # @@ -58,8 +58,8 @@ class ClusteredNetwork: def __init__(self, sim_dict, net_dict, stim_dict): """Initialize the ClusteredNetwork object. - Parameters are given and explained in the files network_params.py, - sim_params.py and stimulus_params.py. + Parameters are given and explained in the files network_params_EI.py, + sim_params_EI.py and stimulus_params_EI.py. Parameters ---------- diff --git a/pynest/examples/EI_clustered_network/network_params.py b/pynest/examples/EI_clustered_network/network_params_EI.py similarity index 97% rename from pynest/examples/EI_clustered_network/network_params.py rename to pynest/examples/EI_clustered_network/network_params_EI.py index c40eb9cb48..bf7c69e1e3 100644 --- a/pynest/examples/EI_clustered_network/network_params.py +++ b/pynest/examples/EI_clustered_network/network_params_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# network_params.py +# network_params_EI.py # # This file is part of NEST. # @@ -20,7 +20,7 @@ # along with NEST. If not, see . """PyNEST EI-clustered network: Network Parameters ------------------------------------------------- +-------------------------------------------------- A dictionary with parameters defining the network and neuron parameters. diff --git a/pynest/examples/EI_clustered_network/run_simulation.py b/pynest/examples/EI_clustered_network/run_simulation_EI.py similarity index 98% rename from pynest/examples/EI_clustered_network/run_simulation.py rename to pynest/examples/EI_clustered_network/run_simulation_EI.py index ecafa112df..1aaadceed8 100644 --- a/pynest/examples/EI_clustered_network/run_simulation.py +++ b/pynest/examples/EI_clustered_network/run_simulation_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# run_simulation.py +# run_simulation_EI.py # # This file is part of NEST. # diff --git a/pynest/examples/EI_clustered_network/sim_params.py b/pynest/examples/EI_clustered_network/sim_params_EI.py similarity index 94% rename from pynest/examples/EI_clustered_network/sim_params.py rename to pynest/examples/EI_clustered_network/sim_params_EI.py index 30ac2cd330..d59d57391b 100644 --- a/pynest/examples/EI_clustered_network/sim_params.py +++ b/pynest/examples/EI_clustered_network/sim_params_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# sim_params.py +# sim_params_EI.py # # This file is part of NEST. # @@ -20,7 +20,7 @@ # along with NEST. If not, see . """PyNEST EI-clustered network: Simulation Parameters ------------------------------------------------- +----------------------------------------------------- A dictionary with parameters defining the simulation. diff --git a/pynest/examples/EI_clustered_network/stimulus_params.py b/pynest/examples/EI_clustered_network/stimulus_params_EI.py similarity index 94% rename from pynest/examples/EI_clustered_network/stimulus_params.py rename to pynest/examples/EI_clustered_network/stimulus_params_EI.py index f5110a11e5..687d557aa7 100644 --- a/pynest/examples/EI_clustered_network/stimulus_params.py +++ b/pynest/examples/EI_clustered_network/stimulus_params_EI.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# stimulus_params.py +# stimulus_params_EI.py # # This file is part of NEST. # @@ -20,7 +20,7 @@ # along with NEST. If not, see . """ PyNEST EI-clustered network: Stimulus Parameters ------------------------------------------------ +----------------------------------------------------- A dictionary with parameters for an optinal stimulation of clusters.